1-171090009-C-G

Position:

• chr1-171090009-C-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The ENST00000653116.1(ENSG00000231424):​n.542+78095G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 151,684 control chromosomes in the GnomAD database, including 6,963 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

• Frequency: Genomes: 𝑓 0.29 (6963 hom., cov: 31)
• Consequence: ENSG00000231424 ENST00000653116.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650

Genes affected

ENSG00000231424 (HGNC:40240):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BP6: Variant 1-171090009-C-G is Benign according to our data. Variant chr1-171090009-C-G is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000231424	ENST00000653116.1	n.542+78095G>C		intron_variant
ENSG00000231424	ENST00000664920.1	n.681+31741G>C		intron_variant
ENSG00000231424	ENST00000669750.1	n.533+78095G>C		intron_variant
ENSG00000231424	ENST00000670085.1	n.371+78095G>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44518 AN: 151570 Hom.: 6943 Cov.: 31

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.274

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.294 AC: 44564 AN: 151684 Hom.: 6963 Cov.: 31 AF XY: 0.299 AC XY: 22139 AN XY: 74114

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.289

Gnomad4 EAS AF: 0.576

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.276

Alfa AF: 0.170 Hom.: 359

Bravo AF: 0.293

Asia WGS AF: 0.438 AC: 1517 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.89
DANN	Benign	0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1736560; hg19: chr1-171059150;